segment

Segmentation: Normalization of SVs into disjointed genomic regions

For SVs with a span in the genome (currently only DELs), split the overlaps into disjointed regions. This is an experimental tool that explores the possibility of assisting SV association analysis.

This tool adds an INFO field SEGCNT which holds the number of original SVs that overlap the newly reported region. It also adds a FORMAT field SEG, which is the 'allele coverage' per-sample. For example, if a sample has two overlapping heterozygous deletions, the shared region will have SEG=2. If the two deletions were homozygous then SEG=4.

In the below example, we have three deletions found across three samples.

The segment added annotations for the regions would then be:

Region	INFO/SEGCNT	S1/SEG	S2/SEG	S3/SEG
A	1	2	0	0
B	2	2	1	0
C	3	2	2	2
D	2	2	1	0
E	1	0	1	0